Functional organization of the eukaryotic genome

All eukaryotic genomes, regardless of their size, are greatly compressed inside the cell nucleus. The first level of compaction depends on the nucleosomes -the basic units of chromatin- which are made up of 147 base pairs of DNA wrapped around a histone octamer. Each human diploid nucleus contains 2 meters of DNA and around 30 million nucleosomes. The genome a haploid yeast spans 5 mm and is packed by 80000 nucleosomes, approximately.

In addition to their structural function, nucleosomes control genome processes by modulating the access of regulatory proteins to DNA or through the epigenetic modification of histones. This regulatory function depends on the precise positioning of nucleosomes relative to the DNA sequence. Nucleosome positioning is regulated by chromatin remodeling complexes, the binding of trancription factors and the DNA sequence itself.

In our laboratory, we are studying how the DNA sequence specifies the position of nucleosomes in the genome. We use species of the yeasts Schizosaccharomyces and Saccharomyces as model systems and biochemical, genetic, genomic and bioinformatic experimental approaches. In recent years, we have reported that the 147 nucleotides of mononucleosomal DNA adopt a well-defined distribution pattern that we have called nucleosomal signatures. Despite the high degree of phylogenetic conservation of histones, nucleosomal signatures differ even among species of the same genus (Quintales et al. 2015) (Figure 1A) raising the question of what could be their biological significance.

Through genomic and bioinformatic approaches, we have shown that nucleosomal signatures contain information to direct the positioning of nucleosomes in chromosomes in vivo. By using this information, we have designed synthetic DNA molecules capable of positioning nucleosomes with the same periodicity than the host genome where they integrate. It is equally possible to remaster genes of an organism through the incorporation of the nucleosomal signature of a different host genome by selecting synonymous codons such that the ectopic gene adopts the nucleosomal organization of the recipient genome while maintaining the expression of the original protein (González et al. 2016) (Figure 1B).

The design of DNA molecules capable of driving their own nucleosomal organization opens the possibility of modifying specific chromatin regions to study its impact on transcriptional regulation, genome stability and the landscape of epigenetic modifications. These approaches are also relevant to the fields of synthetic biology and genome design and could be used to optimize genes and expression vectors of interest in biotechnology. We are currently exploring these possibilities in our laboratory

Image description

Nucleosomal signatures and nucleosomal organization
A) Nucleosomal signatures of the four nucleotides (adenine, green; thymine, red; citosine, blue; guanine, black) along mononucleosomal DNA of Schizosaccharomyces pombe, S. octosporus, S.s japonicus and Saccharomyces cerevisiae. X-axis indicates the distance in nucleotides from the central position of mononucleosomal DNA (0). Ellipses represent nucleosomes.
B) Diagramme of nucleosomal signatures in orthologous genes of two different species. It shows the transcription initiation (white arrows), nucleosome positioning and the proteins encoded by each gene. When the gene of Species 2 is introduced in the genome of Species 1, nucleosomes adopt an irregular pattern (non positioned nucleosomes). Incorporating information from the nucleosomal signature of Species 1 into the gene of Species 2 through the use of synonymous codons, nucleosomes adopt the organization of Species 1 while they still expresses the original protein of Species 2.

Image description

Group members

Francisco Antequera Research Professor (CSIC)
Laura Durán Postdoctoral
Alicia García Postdoctoral
Loreto Megido PhD Student
Laura Rodríguez PhD Student
Mar Sánchez Specialized Technician
Rodrigo Santamaría Tenured Professor (USAL)
Isabel Vaquero PhD Student


Francisco Antequera
Laboratory 2.5

Recent publications

García A, Durán L, Sánchez M, González S, Santamaría R, Antequera F. (2024)
Asymmetrical nucleosomal DNA signatures regulate transcriptional directionality.
Cell Reports 43: 113605
Doi: 10.1016/j.celrep.2023.113605
Schindler D, Walker R; Jiang S, Brooks A, Wang Y, Mueller C, Cockram C, Luo Y, García A, Schraivogel D, Mozziconacci J, Pena N, Assari M, Sanchez M, Zhao Y, Ballerini A, Blount B, Cai J, Ogunlana L, Liu W, Joensson K, Abramczyk D, Garcia-Ruiz E, Turowski T, Swidah R, Ellis T, Pan T, Antequera F, Shen Y, Nieduszynski C, Koszul R, Dai J, Steinmetz L, Boeke J, Cai Y. (2023)
Design, construction, and functional characterization of a tRNA neochromosome in yeast.
Cell 186: 1-17
Doi: 10.1016/j.cell.2023.10.015
Ramos F, Durán L, Sanchez M, Campos A, Hernández-Villamor D, Antequera F*, Clemente-Blanco A*. (2022)
Genome-wide sequencing analysis of Sgs2, Exo1, Rad51, and Srs2 in DNA repair by homologous recombination.
Cell Reports 38: 1-17 (*Co-corresponding authors)
Doi: 10.1016/j.celrep.2021.110201
García J, Lazar-Stefanita L, Gutierrez-Escribano P, Thierry A, García A, González S, Sánchez M , Jarmuz A, Montoya A, Dore M, Kramer H, Mehdi Karimi M, Antequera F, Koszul R, Aragon L. (2019)
FACT mediates cohesin function on chromatin.
Nature Struct. Mol. Biol. 26: 970-979
Doi: 10.1038/s41594-019-0307-x
Santamaría R, Therón R, Durán L, García A, González S, Sánchez M and Antequera F (2018)
Genome-wide search of nucleosome patterns using visual analytics
Bioinformatics 1-8
Doi: 10.1093/bioinformatics/bty971
González S, García A, Vázquez E, Serrano R, Sánchez M, Quintales L and Antequera F (2016)
Nucleosomal signatures impose nucleosome positioning in coding and non-coding sequences in the genome
Genome Research 26: 1532-1543
Doi: 10.1101/gr.207241.116
Quintales L, Soriano I, Vázquez E, Segurado M and Antequera F (2015)
A species-specific nucleosomal signature defines a periodic distribution of amino acids in proteins
Open Biology 5: 140218
Doi: 10.1098/rsob.140218
Castel E, Ren J, Bhattacharjee S, Chang A, Sánchez M, Valbuena A, Antequera F & Martienssen R (2014)
Dicer promotes transcription termination at sites of replication stress to maintain genome stability
Cell 159: 572-583
Doi: 10.1016/j.cell.2014.09.031

Research grants